Question: Tools for genotyping using whole genome re-sequencing data with limited coverage (GBS)
gravatar for Gvj
3.5 years ago by
Gvj440 wrote:

Dear All,

What are the tools (which I can download and use) available for genotyping using low coverage whole genome re-sequencing data? Currently I can find MSG( Andolfatto et al 2011) and MPR(Xie et al 2010) are the two tools which uses HMM to genotype from a very low coverage resequencing ( < 1x coverage). Alternative tool is skim-based GBS(Bayer et al 2016) which basically use sliding window approach. It would be great if you can point out other tools available for this purpose? I am aware about IMPUTE2 and BEAGLE, but since they need a reference panel, its not really useful for me. 

BTW: I am less interested in complexity reduced sequencing for genotyping( such as RAD-seq). 

Thank you in advance

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